Interspecies Sequence Comparison of Brachypodium Reveals How Transposon Activity Corrodes Genome Colinearity

Intergenic sequences evolve rapidly in plant genomes through a process known as genomic turnover. To investigate the influence of DNA-Transposons on genomic turnover, we compared 1 Mbp of orthol-ogous genomic sequences from Brachypodium distachyon and Brachy-podium sylvaticum. We found that B. distachyon and B. sylvaticum diverged approximately 1.7–2.0 million years ago. Of a total of 219 genes identified on the analyzed sequences, 211 were colinear. However, only 24 transposable elements (TEs) out of a total of 451 were orthologous (i.e. inserted in the common ancestor). We characterize in detail 59 insertions and 60 excisions of DNA-Transposons in one or the other species which altered 17% of the intergenic space. The DNA-Transposon excision sites showed complex and highly diagnostic sequence motifs of double-strand break (DSB) repair. DNA-Transposon excision can lead to extensive deletions of hundreds of base pairs (bp) of flanking sequence if the DSB is repaired by "Single Strand Annealing", or insertions of up to several hundred base pairs (bp) of "filler DNA" if the DSB is repaired by "Synthesis Dependent Strand Annealing". In some cases, DSBs were repaired by a combination of both methods. We present a model for the evolution of intergenic sequences in which repair of DSBs upon DNA-Transposon excision is a major factor in the rapid turnover and erosion of intergenic sequences.